LRIG2 p.Pro75=
c.225C>G · VCV4906702
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.2 |
| Overall | ||
| CADD | 9.486 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,866 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000868%
14/1,612,686 alleles · ultra-rare
exomes 14/1,460,424 · genomes 0/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,478 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,239 |
| South Asian | 0.0011% | 91,050 |
| European (non-Finnish) | 0.000424% | 235,993 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- LRIG2
- Protein
- p.Pro75=
- Coding
- c.225C>G
- MANE Select
- NM_014813
- Type
- single nucleotide variant
- Location
- chr1:113073631 (GRCh38)
- Gene constraint
- LOEUF 0.95 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87
- Residue 75
- the lrrnt domain
Similar variants
- LRIG2 p.Arg86Trp Uncertain significance ★★ ⚠ same type
- LRIG2 p.Glu11Ter Uncertain significance ★★ same type
- LRIG2 p.Lys245Arg Uncertain significance ★★ ⚠ same type
- LRIG2 c.2531-22G>A Benign ★★ same type
- LRIG2 p.Ala2= Likely benign ★★ same type
- LRIG2 p.Asp755Glu Benign ★★ same type
- LRIG2 p.Ile155Leu Likely benign ★★ same type
- LRIG2 p.Pro882Leu Likely benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/lrig2-p-pro75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown